Simple Masking/Stencil in the VSE
You can use a mask strip modifier:



In the above example scene1 contains a cube, scene2 contains a Suzanne, and mask_sequence is a black and white mask.

The mask modifier can use either a mask or another VSE strip to modify the transparency of the modified strip according to the darkness of the mask. If you set the blend type of the modified strip to Alpha over, the strip(s) underneath will show through the transparent parts.